%% General info
% All required files can be found in the "Scripts" folder.
% There are two main functions to generate uni-variate and bi-variate plots
% including outputs of regression results which will be stored as text
% files for later processing.
%
% In marmplots.m is a section with experimental filter and fit options
% which are all deactivated. Feel free to experiment with them. Some
% require a parallel processing toolbox license.
%
% The code has been tested in Linux systems only.


%% HowTo
% The main functions have 2 or 3 input strings, defining the data to
% be used for X, Y, and Z, respectively. Inputs are case sensitive.
%
% Available inputs are:
% 'Amy'........Normalized optical density maps of Gallyas based histology
% 'AFe'........Normalized optical density maps of Perl's base histology
% 'F'..........semi-solid pool size fraction
% 'RM0a'.......pseude-first-order contract R*M0a
% 'R1a'........longitudinal relaxation rate of the liquid pool
% 'T1a'........longitudinal relaxation time of the liquid pool
% 'R2a'........transversal relaxation rate of the liquid pool
% 'T2a'........transversal relaxation time of the liquid pool
% 'R2b'........transversal relaxation rate of the semi-solid pool
% 'T2b'........transversal relaxation time of the semi-solid pool
% 'R1obs3T'....observed longitudinal relaxation rate measured at 3T
% 'T1obs3T'....observed longitudinal relaxation time measured at 3T
% 'R1obs7T'....observed longitudinal relaxation rate measured at 7T
% 'T1obs7T'....observed longitudinal relaxation time measured at 7T
% 'R2eff7T'....effective transversal relaxation rate measured at 7T
% 'T2eff7T'....effective transversal relaxation time measured at 7T

% The output structures contain the processed and unprocessed samples for
% the fits as well as the applied masks and all fit results.

%% Add path
addpath Scripts/


%% Example for uni-variate analysis
outputdata_univ = make2Dgraphs('Amy','AFe');


%% Example for bi-variate analysis
outputdata_biv = make3Dgraphs('F','AFe','R1obs3T');